Better later than never.
Since After Effects CC 2015.3 (13.8) you can send your comp to AME queue and render it immédiate with the recently used template.
app.project.renderQueue.canQueueInAME --> false is there is nothing to render in AE
app.project.renderQueue.queueInAME(false); --> false = no render, true = render immedialty in AME
Adobe exemple :
// Scripting support for Queue in AME.
// Requires Adobe Media Encoder 11.0.
{
if (app.project.renderQueue.canQueueInAME == true)
{
// Send queued items to AME, but do not start rendering.
app.project.renderQueue.queueInAME(false);
}
else {
alert("There are no queued item in the Render Queue.");
}
}
My exemple of use :
var resultFile = new File(outputVideoPath + outputVideoName)
var renderQueue = app.project.renderQueue;
var render = renderQueue.items.add(comp);
render.outputModules[1].file = resultFile;
app.project.renderQueue.queueInAME(true);
More details : https://forums.adobe.com/thread/2230567